Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species -- Enhancing Structural Annotation of Yeast Genomes with RNA-Seq Data -- Pathogen Gene Expression Profiling During Infection Using a Nanostring Ncounter Platform -- Comparative Transcriptomics in Yeasts -- Mapping the Transcriptome-Wide Landscape of RBP Binding sites using gPAR-CLIP-seq: Experimental Procedures -- Mapping the Transcriptome-wide Landscape of RBP Binding Sites using gPAR-CLIP-seq: Bioinformatic Analysis -- Translation Analysis at the Genome Scale by Ribosome Profiling -- Biotin-Genomic Run-on (Bio-GRO): A High-Resolution Method for the Analysis of Nascent Transcription in Yeast -- Genome-wide Probing of RNA Structures in Vitro Using Nucleases and Deep Sequencing -- Genome-wide Chromatin Immunoprecipitation in Candida albicans and other Yeasts -- ChIPseq in Yeast Species: from Chromatin Immumoprecipitation to High-Throughput Sequencing and Bioinformatics Data Analyses -- Systematic Determination of Transcription factor DNA-binding Specificities in Yeast -- Generation and Analysis of Chromosomal Contact Maps of Yeast Species -- A Versatile Procedure to Generate Genome-Wide Spatio-Temporal Program of Replication in Yeast Species -- Single-Step Affinity Purification (ssAP) and Mass Spectrometry of Macromolecular Complexes in the Yeast S. cerevisiae -- Label-Free Quantitative Proteomics in Yeast -- Profiling of Yeast Lipids by Shotgun Lipidomics -- Identification of Links between Cellular Pathways by Genetic Interaction Mapping (GIM) -- On The Mapping of Epistatic Genetic Interactions in Natural Isolates: Combining Classical Genetics and Genomics -- Experimental Evolution and Resequencing Analysis of Yeast -- Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs using Arboretum -- Predicting Gene and Genomic Regulation in Saccharomyces cerevisiae, using the YEASTRACT Database: A Step By Step Guided Analysis.

This volume provides a collection of protocols for the study of DNA-DNA contact maps, replication profiles, transcription rates, RNA secondary structures, protein-RNA interactions, ribosome profiling and quantitative proteomes and metabolomes. Written for the Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.   Authoritative and practical, Yeast Functional Genomics: Methods and Protocols aims to ensure successful results in the further study of this vital field.